This is a minor release introducing changes meant to focus S3 methods and
utility functions around two core classes: causal_model and model_query.
Our aim is to improve the user experience of CausalQueries by focusing
user facing functionality more clearly around the workflow of making, updating,
querying and inspecting causal models.
With respect to causal_model objects this release introduces more expressive
and concise S3 summary and print methods for the causal_model class and its
internal objects. Updates to the grab() and inspect() functions streamline
access to objects contained within a causal_model, facilitating more advanced
use-cases or deeper review.
This release introduces the model_query class along with S3 summary, print and
plot methods for a more seamless querying workflow.
Finally, this release removes dependency on dagitty, restoring compatibility of
CausalQueries with systems on which V8 JavaScript WASM is not supported.
The summary() method for objects of class causal_model now supports an
include argument allowing users to specify additional objects internal
to the causal_model object for which they would like to have summaries
appended to the main output of summary(). Summaries have additionally been
made more informative and readable. Please see ?summary.causal_model for
extensive documentation on the new functionality.
Internal objects of a causal_model instance can now be returned quietly
via grab() eliminating the need to interact with a causal_model instance
directly.
The newly introduced model_query class comes with a print, summary and plot
method. plot() generates a coefficient plot with credible intervals for
evaluated queries.
This is a patch release fixing a bug in the print.model_query() S3 method that
occurred when querying models using paramters.
Accessing causal-model objects via get_ methods e.g. get_nodal_types(), get_parameters is no longer supported. Objects may now be accessed via a unified syntax through the inspect() function (see New Functionality).
The following functions are no longer exported:
get_causal_types()get_nodal_types()get_all_data_types()get_event_probabilities()get_ambiguities_matrix()get_parameters()get_parameter_names()get_parmap()get_parameter_matrix()get_priors()get_param_dist()get_type_prob_multiple()inspect()causal-model objects can now be accessed via inspect() like so:
inspect(model, "parameters_df")
See documentation for an exhaustive list of accessible objects. causal-model objects now additionally come with dedicated print methods returning short informative summaries of the given object.
A summary of parameter values and convergence information produced by the update_model() Stan model can now be accessed via:
inspect(model, "stan_summary")
Advanced model diagnostics on raw Stan output via external packages is possible by saving the stan_fit object when updating. This is facilitated via the keep_fit option in update_model():
model <- make_model("X -> Y") |>
update_model(data, keep_fit = TRUE)
model |> inspect("stanfit")
nodal_types to make_model() now implements correct error handlingPreviously this make_model("X -> Y" , nodal_types = list(Y = c("0", "1"))) was
permissible leading to setting nodal_types:
$X
NULL
$Y
[1] "0" "1"
This led to undefined behavior and unhelpful downstream error messages.
When passing nodal_types to make_model() users are now forced to specify
a set of nodal_types on each node.
query_distribution() are no longer overwrites type distribution internallymake_model()Previously hyphenated names would not throw an error and be corrupted
silently through the conversion of model definition strings into
dagitty objects.
make_model("institutions -> political-inequality")
Statement:
[1] "institutions -> political-inequality"
DAG:
parent children
1 institutions political
Checks for correct variable naming are now reinstated.
Calls to sapply() have ben replaced with vapply() wherever possible to
enforce type safety.
Looping via index has been replaced by range based looping wherever possible to guard against 0 length exceptions.
goodpractice::gp()goodpractice code improvements have been implemented.
query_distribution() now supports the use of multiple queries in one function call and thus returns a DataFrame
of distribution draws instead of a single numeric vector.
query_distribution(): now supports the specification of multiple queries and givens to be evaluated on a single model in one function call.
model <- make_model("X -> Y")
query_distribution(model,
query = list("(Y[X=1] > Y[X=0])", "(Y[X=1] < Y[X=0])"),
given = list("Y==1", "(Y[X=1] <= Y[X=0])"),
using = "priors")|>
head()
query_model(): now supports the specification of multiple models to evaluate a set of queries on in one function call.
models <- list(
M1 = make_model("X -> Y"),
M2 = make_model("X -> Y") |> set_restrictions("Y[X=1] < Y[X=0]")
)
query_model(
models,
query = list(ATE = "Y[X=1] - Y[X=0]", Share_positive = "Y[X=1] > Y[X=0]"),
given = c(TRUE, "Y==1 & X==1"),
using = c("parameters", "priors"),
expand_grid = FALSE)
query_model(
models,
query = list(ATE = "Y[X=1] - Y[X=0]", Share_positive = "Y[X=1] > Y[X=0]"),
given = c(TRUE, "Y==1 & X==1"),
using = c("parameters", "priors"),
expand_grid = TRUE)
This eliminates the need for redundant function calls when querying models and substantially improves computation time as computationally expensive function calls to produce data structures required for querying are now reduced to a minimum via redundancy elimination and caching.
realise_outcomes(): specifying the node option now produces a DataFrame detailing how the specified node responds to its parents in the presence or absence of do operations. This produces a reduced form of the usual realise_outcomes() output detailing all causal-types; and aids in the interpretation of both nodal- and causal-types. This update resolves previous bugs and errors relating to specification of nodes with multiple parents in the node option.
model <- make_model("X1 -> M -> Y -> Z; X2 -> Y") |>
realise_outcomes(dos = list(M = 1), node = "Y")
Previously set_parameters() and set_priors() would default applying changes in the order in which parameters appeared in the parameters_df DataFrame; regardless of the order in which changes were specified in the aforementioned functions.
Calling:
model <- make_model("X -> Y")
set_priors(model, alphas = c(3,4), nodal_type = c("10",00))
would results in the following parameters_df.
param_names node gen param_set nodal_type given param_value priors
<chr> <chr> <int> <chr> <chr> <chr> <dbl> <dbl>
1 X.0 X 1 X 0 "" 0.5 1
2 X.1 X 1 X 1 "" 0.5 1
3 Y.00 Y 2 Y 00 "" 0.25 3
4 Y.10 Y 2 Y 10 "" 0.25 4
5 Y.01 Y 2 Y 01 "" 0.25 1
6 Y.11 Y 2 Y 11 "" 0.25 1
Now changes to parameters values get applied in the order specified in the function call; resulting in the following parameters_df for the above example:
param_names node gen param_set nodal_type given param_value priors
<chr> <chr> <int> <chr> <chr> <chr> <dbl> <dbl>
1 X.0 X 1 X 0 "" 0.5 1
2 X.1 X 1 X 1 "" 0.5 1
3 Y.00 Y 2 Y 00 "" 0.25 4
4 Y.10 Y 2 Y 10 "" 0.25 3
5 Y.01 Y 2 Y 01 "" 0.25 1
6 Y.11 Y 2 Y 11 "" 0.25 1
Additionally we have implemented helpful warnings for when instructions identifying parameters to be updated are under specified. This is particularly useful when setting priors or parameters on models with confounding as changes may inadvertently be applied across param_sets.
Previously updating models with censored types would fail as 0s in the w vector induced by censoring would evaluate to -Inf as the Stan MCMC algorithm began sampling from the posterior of the multinational distribution.
We resolved this issue by pruning the w vector when the multinomial is run. This preserves the true
w vector (event probabilities without censoring) while still updating with the censored data-
Previously wildcards in set_restrictions() were erroneously interpreted as valid nodal types, leading to errors and undefined behavior. Proper unpacking and mapping of wildcards to existing nodal types has been restored.
Previously misspecifications in queries like Y[X==1]=1 would lead to undefined behavior when mapping queries to nodal or causal types. We now correct misspecified queries internally and warn about the misspecification. For example; running:
model <- CausalQueries::make_model("X -> Y")
get_query_types(model, "Y[X=1]=1")
now produces
Causal types satisfying query's condition(s)
query = Y[X=1]==1
X0.Y01 X1.Y01
X0.Y11 X1.Y11
Number of causal types that meet condition(s) = 4
Total number of causal types in model = 8
Warning message:
In check_query(query) :
statements to the effect that the realization of a node should equal some value should be specified with `==` not `=`.
The query has been changed accordingly: Y[X=1]==1
Previously a parameter matrix P that was attached to a causal_model object could not be overwritten. Overwrites are now possible.
realise_outcomes()We achieved a ~100 fold speed gain in the realise_outcomes() functionality. Nodal types on a given node are generated as the Cartesian product of parent realizations. Consider the meaning of nodal types on a node $Y$ with 3 parents $[X1,X2,X3]$:
| X1 | X2 | X3 | |------|------|------| | 0 | 0 | 0 | | 1 | 0 | 0 | | 0 | 1 | 0 | | 1 | 1 | 0 | | 0 | 0 | 1 | | 1 | 0 | 1 | | 0 | 1 | 1 | | 1 | 1 | 1 |
Each row in the above DataFrame corresponds to a digit in Y's nodal types. The first digit of each nodal type of $Y$ (see first row above), corresponds to the realization of $Y$ when $X1 = 0, X2 = 0, X3 = 0$. The fourth digit of each nodal type of $Y$ (see fourth row above), corresponds to the realization of $Y$ when $X1 = 1, X2 = 1, X3 = 0$. Finding the position of the realization value of $Y$ in a nodal type given parent realizations is equivalent to finding the row number in the Cartesian product DataFrame. By definition of the Cartesian product, the number of consecutive 0 or 1 elements in a given column is $2^{columnindex}$, when indexing columns from 0. Given a set of parent realizations $R$ indexed from 0, the corresponding row in a number in a DataFrame indexed from 0 can thus be computed via:
$$row = (\sum_{i = 0}^{|R| - 1} (2^{i} \times R_i))$$.
We implement a fast C++ version of this computing powers of 2 via bit shifting.
Stan updateWe updated to the new array syntax introduced in Stan v2.33.0